Hi, I've been unsuccessful in installing my own packages 'planar' and 'cda' from source, since I updated my MacBook Pro to Yosemite. I have the latest stable binary of R from CRAN, re-installed the latest Xcode via AppStore, got gfortran from http://r.research.att.com/, and I still get a compilation error. My guess is that I have inadvertently carried over an older version of gcc from the previous OS, and R is looking for a different one. The error message for planar goes like this,
R CMD INSTALL planar * installing to library ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library’ * installing *source* package ‘planar’ ... ** package ‘planar’ successfully unpacked and MD5 sums checked ** libs clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o planar.so collection.o gaussian_beam.o hcubature.o multilayer.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2 -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: directory not found for option '-L/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2' ld: library not found for -lquadmath clang: error: linker command failed with exit code 1 (use -v to see invocation) make: *** [planar.so] Error 1 ERROR: compilation failed for package ‘planar’ * removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/planar’ * restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/planar’ ------------------------- Indeed, the directory "/usr/local/lib/gcc/x86_64-apple-darwin13.0.0/4.8.2" does not exist. The closest thing seems to be "/usr/local/lib/gcc/i686-apple-darwin8", > ls -R /usr/local/lib/gcc | tree |-------i686-apple-darwin8 |---------4.2.3 |-----------finclude |-----------x86_64 |-------powerpc-apple-darwin8 |---------4.2.3 |-----------finclude |-----------ppc64 Could it be enough to set a few compilation flags to point R to the right gcc libraries? (not sure how) Best regards, baptiste ----- session info ----- > sessionInfo() R version 3.2.0 Patched (2015-05-21 r68393) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.3 (Yosemite) locale: [1] en_NZ.UTF-8/en_NZ.UTF-8/en_NZ.UTF-8/C/en_NZ.UTF-8/en_NZ.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_3.2.0 > Sys.getenv() __CF_USER_TEXT_ENCODING 0x1F5:0x0:0x0 Apple_PubSub_Socket_Render /private/tmp/com.apple.launchd.2pqH8flWmK/Render DISPLAY /private/tmp/com.apple.launchd.e31xJhIRZF/org.macosforge.xquartz:0 DYLD_FALLBACK_LIBRARY_PATH /Users/baptiste/lib:/usr/local/lib:/usr/lib::/Library/Frameworks/R.framework/Resources/lib EDITOR vi GIT_ASKPASS rpostback-askpass HOME /Users/baptiste LANG en_NZ.UTF-8 LC_CTYPE en_NZ.UTF-8 LN_S ln -s LOGNAME baptiste MAKE make PAGER /usr/bin/less PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/texbin:/usr/local/bin:/opt/X11/bin PDFLATEX /usr/texbin/pdflatex R_BROWSER /usr/bin/open R_BZIPCMD /usr/bin/bzip2 R_DOC_DIR /Library/Frameworks/R.framework/Resources/doc R_GZIPCMD /usr/bin/gzip R_HOME /Library/Frameworks/R.framework/Resources R_INCLUDE_DIR /Library/Frameworks/R.framework/Resources/include R_LIBS_SITE R_LIBS_USER ~/Library/R/3.2/library R_PAPERSIZE a4 R_PDFVIEWER /usr/bin/open R_PLATFORM x86_64-apple-darwin13.4.0 R_PRINTCMD lpr R_QPDF /Library/Frameworks/R.framework/Resources/bin/qpdf R_RD4PDF times,inconsolata,hyper R_SESSION_TMPDIR /var/folders/nh/4719qghd3bz60tc_n28062840000gn/T//RtmpNqgTMe R_SHARE_DIR /Library/Frameworks/R.framework/Resources/share R_SYSTEM_ABI osx,gcc,gxx,gfortran,? R_TEXI2DVICMD /usr/local/bin/texi2dvi R_UNZIPCMD /usr/bin/unzip R_ZIPCMD /usr/bin/zip RMARKDOWN_MATHJAX_PATH /Applications/RStudio.app/Contents/Resources/resources/mathjax-23 RS_RPOSTBACK_PATH /Applications/RStudio.app/Contents/MacOS/rpostback RS_SHARED_SECRET 8dfae406-353d-44e7-bf9a-12efa87271a8 RSTUDIO 1 RSTUDIO_PANDOC /Applications/RStudio.app/Contents/MacOS/pandoc RSTUDIO_SESSION_PORT 33826 RSTUDIO_USER_IDENTITY baptiste SED /usr/bin/sed SHELL /bin/bash SSH_AUTH_SOCK /private/tmp/com.apple.launchd.v82zIG6NDp/Listeners TAR /usr/bin/tar TMPDIR /var/folders/nh/4719qghd3bz60tc_n28062840000gn/T/ USER baptiste XPC_FLAGS 0x0 XPC_SERVICE_NAME 0 [[alternative HTML version deleted]] _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-mac